BIOL 3000 Chromatin and DNA Packaging

How many chromosome pairs are in each cell?

23

How many meters of DNA is in each cell?

~2 meters

Chromatin?

A complex of DNA and protein (histones) found in eukaryotic cells

Euchromatin

Lightly packed chromatin rich in gene concentration and is most often under active transcription

Heterochromatin

Tightly packed chromatin consists mainly of genetically inactive sequences. Not a lot of genes are used

Constitutive heterochromatin

VERY gene poor; centromeres and telomeres

ALWAYS constitutive

Facultative heterochromatin

Can be gene silencing; Barr bodies

Has the ability to be both euchromatin or heterochromatin

Coding regions

Regions we are actually ablet to read

Folded Fiber Model (E.J. Dupraw)

Has whole mounts of human white blood cells

Found few or no free fiber ends and concluded each chromatid must consist of a single fiber

Extensive folding of Type B forms chromatin

Replication from each end toward the centromere

Thought to have folded upon itself, like yarn

Issues to the Folded Fiber Model

E.J. Dupraw did not give any reasons to how some chromatin went from here to there

Nucleosome Model (R.D. Kornberg, P. Oudet)

Most commonly accepted model for DNA packaging

Nucleosome

The simplest packaging structure of all eukaryotic chromatin localized areas of transcription; better fit for protein biosynthesis

Has a protein core that has DNA that wraps aroundH

Histone

Protein that is heterochromatin and constitutive. There are two types: core and linker

How many histones are in a nucleosome

9

Core histones

H2A, H2B, H3, H4 (2x of each)

Consists of approximately 120 amino acids each

Highly conserved during evolution

In combination with the core particle

VERY basic in charge (approx. 25% Lysine and Arginine)

Linker histone

H1

NOT PART OF CORE but part of nucleosome

Consist of approximately 200 amino acids

Tissue specific expression and not highly conserved

Loosely associated with core particle

Only one in nucleosome

Formation of the nucleosome

Primary packaging of the chromatin (least packaging reduces DNA length) 200 bp of DNA (146bp wrap the core; 54 bp link to the next nucleosome - linker DNA)

Reduces DNA length by ~7 times

Linear arrangement

10 nm Fiber

10nm Fiber

Primary packaging of the chromatin

Supercoiling of DNA - Formation of the solenoid

H1 Histone responsible for packaging

Solenoid/30nm Fiber

Supercoiling reduces length of DNA by ~7 times

Solenoid

30nm Fiber

Helical coiling of 10nm fibers consisting of 6 nucleosomes (54 histones)

H1 Histone function

Binds to two distinct regions: linker DNA and a portion of the 146 bp core

Will compact DNA to 40x

Binds to both linker DNA and central core DNA and induces tighter DNA wrapping around histones

Supercoiling of DNA - Formation of the Zig-Zag model

The DNA backbone is not flexible enough to bend between the nucleosomes, so the straight linker DNA connects opposite nucleosomes. The zig-zag allows for greater compaction.

DNA is in the middle and does not have bends on the side

Can both solenoid and zig-zag topologies be present in chromatin fiber simultaneously?

Yes, it is experimentally shown. They are both legitimate models

Higher order coiling

300nm

“Chromatin loops”

Built around a scaffold of Topoisomerase II

Compaction level of Euchromatin (allowing us to have access to the material)

Final Condensation

700nm Fiber

Metaphase chromosome

DNA diameter is ~700nm

A spiral scaffold composed of Topoisomerase II and about 15 non-histone proteins

Compaction level of heterochromatin (cannot access DNA material)

Chromatin Formation and Cell Cycle

Karyotype

Picture of metaphase chromosomes in the nucleus of eukaryotic cells

Based off of chromosome size, centromere position, heterochromatin v.s. euchromatin